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SNARE-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Profilin-like [ 55769] (10)
Superfamily:   SNARE-like [ 64356] (4)
Families:   Synatpobrevin N-terminal domain [ 64357] (2)
  Sedlin (SEDL) [ 82767]
  Clathrin coat assembly domain [ 75521] (2)
  SRP alpha N-terminal domain-like [ 90019] (2)


Superfamily statistics
Genomes (504) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,930 12,400 11
Proteins 11,869 12,365 11


Functional annotation
General category General
Detailed category Protein interaction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)biological regulation0.98131Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.083920.03989Least InformativeInherited
Biological Process (BP)cellular localization0.000000063220Moderately InformativeDirect
Biological Process (BP)regulation of localization0.42890.3394Moderately InformativeInherited
Biological Process (BP)single organism signaling0.17711Moderately InformativeInherited
Biological Process (BP)single-organism transport11Moderately InformativeInherited
Biological Process (BP)organelle organization0.3890.0002169Moderately InformativeInherited
Biological Process (BP)nitrogen compound transport0.62450.1178Moderately InformativeInherited
Biological Process (BP)organic substance transport10.8997Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.055070.01043Moderately InformativeInherited
Biological Process (BP)cell communication0.26861Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.065040.8119Moderately InformativeInherited
Biological Process (BP)cell-cell signaling0.00013710.0004155InformativeDirect
Biological Process (BP)vesicle-mediated transport0.000000000034260InformativeDirect
Biological Process (BP)secretion by cell0.00011260InformativeDirect
Biological Process (BP)membrane organization0.0001170InformativeDirect
Biological Process (BP)single-organism intracellular transport0.20810.3551InformativeInherited
Biological Process (BP)organelle localization0.22240.1074InformativeInherited
Biological Process (BP)regulation of neurotransmitter levels0.0000013950.0000001991Highly InformativeDirect
Biological Process (BP)vesicle organization0.0000000053910Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport0.00000075980Highly InformativeDirect
Biological Process (BP)vesicle localization0.000000000044510.000000000005368Highly InformativeDirect
Biological Process (BP)trans-synaptic signaling0.00000037820.00001655Highly InformativeDirect
Biological Process (BP)regulation of lipid localization0.00022050.00004277Highly InformativeDirect
Biological Process (BP)signal release0.000012380.01126Highly InformativeInherited
Molecular Function (MF)binding0.66071Least InformativeInherited
Molecular Function (MF)transporter activity0.047870.06482Moderately InformativeInherited
Molecular Function (MF)molecular function regulator0.031730.1319Moderately InformativeInherited
Molecular Function (MF)guanyl-nucleotide exchange factor activity0.00000057470.000002675Highly InformativeDirect
Molecular Function (MF)protein transporter activity0.0000000026520.0000000000004258Highly InformativeDirect
Cellular Component (CC)membrane0.0000019260Least InformativeDirect
Cellular Component (CC)macromolecular complex0.000000000020020Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.1480.00000000000000914Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.0051990.00003802Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.071560.06583Least InformativeInherited
Cellular Component (CC)vesicle0.000000011230Moderately InformativeDirect
Cellular Component (CC)bounding membrane of organelle00Moderately InformativeDirect
Cellular Component (CC)membrane protein complex0.000000000027610Moderately InformativeDirect
Cellular Component (CC)whole membrane0.0000000000000013540Moderately InformativeDirect
Cellular Component (CC)plasma membrane11Moderately InformativeInherited
Cellular Component (CC)Golgi apparatus00InformativeDirect
Cellular Component (CC)cytoplasmic vesicle part00InformativeDirect
Cellular Component (CC)synapse0.0000036080.00001713InformativeDirect
Cellular Component (CC)endosome0.55930.1079InformativeInherited
Cellular Component (CC)membrane region0.00026480.01299InformativeInherited
Cellular Component (CC)plasma membrane protein complex0.036350.2695InformativeInherited
Cellular Component (CC)Golgi-associated vesicle00Highly InformativeDirect
Cellular Component (CC)synaptic vesicle0.000056160.000000008971Highly InformativeDirect
Cellular Component (CC)coated vesicle00Highly InformativeDirect
Cellular Component (CC)cytoplasmic vesicle membrane0.000003670.00001345Highly InformativeDirect
Cellular Component (CC)tethering complex0.00000000024460.0000000000002498Highly InformativeDirect
Cellular Component (CC)endocytic vesicle0.62230.101Highly InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.03989 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) organelle organization 0.0002169 Moderately Informative Direct
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.3394 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.1178 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.01043 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.8997 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.2815 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.8119 Moderately Informative Inherited
Biological Process (BP) microtubule-based process 0.00003471 Informative Direct
Biological Process (BP) cell-cell signaling 0.0004155 Informative Direct
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) secretion by cell 0 Informative Direct
Biological Process (BP) membrane organization 0 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.3551 Informative Inherited
Biological Process (BP) organelle localization 0.1074 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 0.02611 Informative Inherited
Biological Process (BP) immune effector process 0.005552 Informative Inherited
Biological Process (BP) cell activation 0.01238 Informative Inherited
Biological Process (BP) immune response 0.05468 Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0.0000001991 Highly Informative Direct
Biological Process (BP) myeloid cell activation involved in immune response 0.000001857 Highly Informative Direct
Biological Process (BP) neutrophil mediated immunity 0.0000005603 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.0000000004455 Highly Informative Direct
Biological Process (BP) vesicle organization 0 Highly Informative Direct
Biological Process (BP) neutrophil activation 0.0000005395 Highly Informative Direct
Biological Process (BP) leukocyte degranulation 0.000001055 Highly Informative Direct
Biological Process (BP) single-organism membrane fusion 0.0000000006995 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0 Highly Informative Direct
Biological Process (BP) organelle fusion 0.0000000000001373 Highly Informative Direct
Biological Process (BP) vesicle localization 0.000000000005368 Highly Informative Direct
Biological Process (BP) trans-synaptic signaling 0.00001655 Highly Informative Direct
Biological Process (BP) regulation of lipid localization 0.00004277 Highly Informative Direct
Biological Process (BP) signal release 0.01126 Highly Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0.06482 Moderately Informative Inherited
Molecular Function (MF) molecular function regulator 0.1319 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0.001971 Informative Inherited
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.000002675 Highly Informative Direct
Molecular Function (MF) protein transporter activity 0.0000000000004258 Highly Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) macromolecular complex 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000000000000914 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00003802 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.06583 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.00000006296 Moderately Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0 Moderately Informative Direct
Cellular Component (CC) whole membrane 0 Moderately Informative Direct
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.00001749 Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) cytoplasmic vesicle part 0 Informative Direct
Cellular Component (CC) vacuolar part 0.00000003231 Informative Direct
Cellular Component (CC) synapse 0.00001713 Informative Direct
Cellular Component (CC) endosome 0.1079 Informative Inherited
Cellular Component (CC) membrane region 0.01299 Informative Inherited
Cellular Component (CC) plasma membrane protein complex 0.2695 Informative Inherited
Cellular Component (CC) lytic vacuole 0.01985 Informative Inherited
Cellular Component (CC) lysosomal membrane 0.00002864 Highly Informative Direct
Cellular Component (CC) endoplasmic reticulum-Golgi intermediate compartment 0.00002742 Highly Informative Direct
Cellular Component (CC) Golgi-associated vesicle 0 Highly Informative Direct
Cellular Component (CC) synaptic vesicle 0.000000008971 Highly Informative Direct
Cellular Component (CC) coated vesicle 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.00001345 Highly Informative Direct
Cellular Component (CC) SNARE complex 0 Highly Informative Direct
Cellular Component (CC) tethering complex 0.0000000000002498 Highly Informative Direct
Cellular Component (CC) endocytic vesicle 0.101 Highly Informative Inherited
Cellular Component (CC) late endosome 0.1468 Highly Informative Inherited
Cellular Component (CC) endosome membrane 0.792 Highly Informative Inherited

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Congenital onset0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the face0.1573Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.706Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal nasal morphology0.1424InformativeInherited
Phenotypic Abnormality (PA)Prominent nose0.0003112Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant0.0000032Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.00000687Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00002126Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.00007293Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0001736Least InformativeDirect
Worm Phenotype (WP)larval development variant0.3954Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.4247Least InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.0000000134Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.0006054Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.004861Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.07281Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.0811Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.2064Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.4377Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.5084Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.5766Moderately InformativeInherited
Worm Phenotype (WP)sick0.00009012InformativeDirect
Worm Phenotype (WP)sensillum morphology variant0.0002523InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.0006112InformativeDirect
Worm Phenotype (WP)aldicarb response variant0.001005InformativeInherited
Worm Phenotype (WP)nuclear positioning variant0.001072InformativeInherited
Worm Phenotype (WP)pigmentation variant0.002792InformativeInherited
Worm Phenotype (WP)drug resistant0.003114InformativeInherited
Worm Phenotype (WP)body length variant0.005524InformativeInherited
Worm Phenotype (WP)mitosis variant0.006453InformativeInherited
Worm Phenotype (WP)body width variant0.007566InformativeInherited
Worm Phenotype (WP)alimentary system development variant0.07953InformativeInherited
Worm Phenotype (WP)gonad development variant0.1455InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.1521InformativeInherited
Worm Phenotype (WP)gut granule development variant0.00001256Highly InformativeDirect
Worm Phenotype (WP)molt variant0.0000378Highly InformativeDirect
Worm Phenotype (WP)oocyte septum formation variant0.00007552Highly InformativeDirect
Worm Phenotype (WP)lysosome organization biogenesis variant0.0001138Highly InformativeDirect
Worm Phenotype (WP)dumpy0.0001713Highly InformativeDirect
Worm Phenotype (WP)clear0.0001741Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant0.0002277Highly InformativeDirect
Worm Phenotype (WP)aldicarb resistant0.0003622Highly InformativeDirect
Worm Phenotype (WP)cell secretion variant0.00057Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)intracellular transport0.03094InformativeInherited
Yeast Phenotype (YP)protein transport0.004081Highly InformativeInherited

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)pollen tube cell0.00004486InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.0001199Moderately InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processEndocytosis0InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Biological processExocytosis0.0000001646Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentCell junction0.003035Moderately InformativeInherited
Cellular componentLysosome0.0000007931InformativeDirect
Cellular componentSynapse0.000003188InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
Cellular componentSynaptosome0.000009531Highly InformativeDirect
DomainTransmembrane0.000002771Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Molecular functionLipid-binding0.000001798Moderately InformativeDirect
Post-translational modificationPhosphoprotein0.000002216Least InformativeDirect
Post-translational modificationAcetylation0.00000568Least InformativeDirect
Post-translational modificationPalmitate0.0000000000001431Moderately InformativeDirect
Post-translational modificationMethylation0.000001097Moderately InformativeDirect
Post-translational modificationPrenylation0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011012 SSF64356 Protein matches
Abstract

VAMPs (and its homologue synaptobrevins) define a group of SNARE proteins that contain a C-terminal coiled-coil/SNARE motif, in combination with variable N-terminal domains that are used to classify VAMPs: those containing longin N-terminal domains (~150 aa) are referred to as longins, while those with shorter N-termini are referred to as brevins [PubMed12914952]. Longins are the only type of VAMP protein found in all eukaryotes, suggesting that their longin domain is essential. The longin domain is thought to exert a regulatory function. Longin domains have been shown to share the same structural fold, a profilin-like globular domain consisting of a five-stranded antiparallel beta-sheet that is sandwiched by an alpha-helix on one side, and two alpha-helices on the other (beta(2)-alpha-beta(3)-alpha(2)).

Other families have been shown to contain domains that structurally resemble the VAMP longin domain. An example is the eukaryotic conserved protein, SEDL, which is a component of the transport protein particle (TRAPP), critically involved in endoplasmic reticulum-to-Golgi vesicle transport; mutations in the SEDL gene are associated with an X-linked skeletal disorder, spondyloepiphyseal dysplasia tarda [PubMed12361953]. Another example is the assembly domain of clathrin coat proteins, such as Mu2 adaptin (AP50) and Sigma2 adaptin (AP17), which structurally resemble the longin domain. AP50 and AP17 are two of the proteins that make up the core of AP2, a complex that functions in clathrin-mediated endocytosis [PubMed12086608].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 7 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a SNARE-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 7 hidden Markov models representing the SNARE-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]